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Achieving food security will require closing yield gaps in many regions, including Pakistan. Although fertilizer subsidies have facilitated increased nitrogen (N) application rates, many staple crop yields have yet to reach their maximum potential. Considering that current animal manure and human excreta (bio-supply) recycling rates are low, there is substantial potential to increase the reuse of nutrients in bio-supply. We quantified 2010 crop N, phosphorus (P), and potassium (K) needs along with bio-supply nutrient availability for Pakistani districts, and compared these values to synthetic fertilizer use and costs. We found that synthetic fertilizer use combined with low bio-supply recycling resulted in a substantial gap between nutrient supply and P and K crop needs, which would cost 3 billion USD to fill with synthetic fertilizers. If all bio-supply was recycled, it could eliminate K synthetic fertilizer needs and decrease N synthetic fertilizer needs to 43% of what was purchased in 2010. Under a full recycling scenario, farmers would still require an additional 0.28 million tons of synthetic P fertilizers, costing 2.77 billion USD. However, it may not be prohibitively expensive to correct P deficiencies. Pakistan already spends this amount of money on fertilizers. If funds used for synthetic N were reallocated to synthetic P purchases in a full bio-supply recycling scenario, crop needs could be met. Most recycling could happen within districts, with only 6% of bio-supply requiring between-district transport when optimized to meet national N crop needs. Increased recycling in Pakistan could be a viable way to decrease yield gaps.

Previous studies have suggested that body size and locomotor performance are targets of Darwinian selection in reptiles. However, much of the variation in these traits may derive from phenotypically plastic responses to incubation temperature, rather than from underlying genetic variation. Intriguingly, incubation temperature may also influence cognitive traits such as learning ability. Therefore, we might expect correlations between a reptiles size, locomotor speed and learning ability either due to selection on all of these traits or due to environmental effects during egg incubation. In the present study, we incubated lizard eggs (Scincidae: Bassiana duperreyi) under hot and cold thermal regimes and then assessed differences in hatchling body size, running speed and learning ability. We measured learning ability using a Y-maze and a food reward. We found high correlations between size, speed and learning ability, using two different metrics to quantify learning (time to solution, and directness of route), and showed that environmental effects (incubation temperature) cause these correlations. If widespread, such correlations challenge any simple interpretation of fitness advantages due to body size or speed within a population; for example, survivors may be larger and faster than nonsurvivors because of differences in learning ability, not because of their size or speed.

We give a comprehensive review of Chesson's coexistence theory, summarizing, for the first time, all its fundamental details in one single document. Our goal is for both theoretical and empirical ecologists to be able to use the theory to interpret their findings, and to get a precise sense of the limits of its applicability. To this end, we introduce an explicit handling of limiting factors, and a new way of defining the scaling factors that partition invasion growth rates into the different mechanisms contributing to coexistence. We explain terminology such as relative nonlinearity, storage effect, and growth-density covariance, both in a formal setting and through their biological interpretation. We review the theory's applications and contributions to our current understanding of species coexistence. While the theory is very general, it is not well suited to all problems, so we carefully point out its limitations. Finally, we critique the paradigm of decomposing invasion growth rates into stabilizing and equalizing components: we argue that these concepts are useful when used judiciously, but have often been employed in an overly simplified way to justify false claims.

The stability of complex ecological networks depends both on the interactions between species and the direct effects of the species on themselves. These self-effects are known as self-regulation when an increase in a species abundance decreases its per-capita growth rate. Sources of self-regulation include intraspecific interference, cannibalism, time-scale separation between consumers and their resources, spatial heterogeneity and nonlinear functional responses coupling predators with their prey. The influence of self-regulation on network stability is understudied and in addition, the empirical estimation of self-effects poses a formidable challenge. Here, we show that empirical food web structures cannot be stabilized unless the majority of species exhibit substantially strong self-regulation. We also derive an analytical formula predicting the effect of self-regulation on network stability with high accuracy and show that even for random networks, as well as networks with a cascade structure, stability requires negative self-effects for a large proportion of species. These results suggest that the aforementioned potential mechanisms of self-regulation are probably more important in contributing to the stability of observed ecological networks than was previously thought.

Most of the world’s ecosystems suffer from stress caused by human activities such as habitat destruction, fragmentation, overexploitation of species and climate change. These factors affect the reproduction and/or survival of individual species as well as interactions between species in ecological communities. Forthcoming effects of this are altered abundances, direct species loss, and indirect cascading extinctions, with yet largely unknown consequences on community structure and functioning. Today, biodiversity loss is of global concern since human society and welfare depend upon resources and services provided by ecosystems. The importance of considering entire ecological communities as a target for conservation and management has been increasingly recognized due to the interdependencie of species. Our ability to make predictions of the response of ecological communities to stress and biodiversity loss is in need of a deeper understanding of how structure and dynamical processes contributes to the functioning and stability of a community. In this thesis I use mathematical theory and dynamical models to study the response of community structure and resilience to a variety of disturbances affecting species and species interactions, ranging from small perturbations (Papers I-II) to large perturbations (species extinctions, Papers IIIIV).

In Paper I we develop Community Sensitivity Analysis (CSA) as an analytical tool to study how a small permanent perturbation to the intrinsic growth rate, or mortality rate, of species is expected to affect i) the resilience (return rate) and ii) the structure (distribution of species equilibrium abundances) of an ecological community. Species interactions are described using Lotka-Volterra predator-prey dynamics. We apply CSA on the pelagic food webs of Lake Vättern and the Baltic Sea, respectively, and find that a change in the mortality rate of large-bodied species has a higher impact on community resilience and structure, compared to a perturbation to small-bodied species. However, analyzing the effect of a proportional change to the growth or mortality rate of species (elasticity analysis) shows that smallbodied species have proportionally larger effects on species equilibrium abundances, but not on resilience. CSA can also be used to study the effect of permanent (absolute or proportional) changes to inter- and intraspecific interaction strengths. For the two pelagic systems used in this study, CSA reveal that changes in the effect of a prey on its consumer tend to affect community structure and resilience significantly more than changes in the effect of a predator on its prey.

In Paper II we assess the importance of rare species for the structure and resilience of ecological communities. First we show analytically, for a two species predator-prey system, that a change in the intrinsic growth rate of the rare species affect resilience more than a change in the growth rate of the common species. To test the generality of these results we next apply CSA on complex model food webs. In the analysis we distinguish between four trophic groups, each including only species with a similar trophic position, to separate the effect of abundance from the trophic position of species. Using mixed effect models we find support for our analytical predictions. More precisely, we find a strong negative relationship between the importance (sensitivity) of a species and its equilibrium abundance within all consumer groups and a weaker, but significant, relationship for producer species. The results from this study suggest that rare species can act as keystones through their effect on both community resilience and community structure, regardless of its trophic position.

In Paper III we evaluate the risk of food web collapse caused by different trait-based extinction scenarios. In previous studies, groups of species, e.g. rare species, large-bodied species and top predators, have been identified to be relatively more prone to extinctions and other studies have found that extinctions of such species have comparably small effects on the remaining community. Using mathematical models of species dynamics we study the response of ecological communities to species removal (i.e. the proportion of species needed to be primarily removed to cause a 50% reduction in species richness, R50) when species are sequentially removed from the food web based on eight different traits. We show, contrary to some previous studies of sequential extinction simulations, that communities can be very vulnerable to realistic species loss. We furthermore find that the response of communities seems to depend on whether the extinction sequence follows a bottom-up or top-down direction, making it difficult to identify one particular extinction sequence as the most important/severe sequence.

Finally, in Paper IV we aim to identify traits of species that can be used to identify keystone species, in terms of causing the highest proportion of secondary extinctions following their loss, in food webs with different degree of disassembly. Moreover, we analyze if the loss of a species that triggers a cascade of many secondary extinctions are the same species being identified as a keystones using Community Sensitivity Analysis. To answer these questions we randomly remove species from a set of 100 model communities. We analyze the relationship between the number of secondary extinctions following the randomly removed species and a range of species traits in communities where i) 75-100% of the initial number of species remain, ii) 50-75% of all species remain, iii) 25-50% of all species remain and iv) only 0-25% of all species remain. We find that the variation in secondary extinctions explained using species traits increases when the degree of food web disassembly and food web connectance are taken into account. The most important trait varies for different degrees of food web disassembly and also depends on whether basal species can go primarily extinct or not. However, due to correlation between most important traits, we conclude that the key status of different traits is rather robust against structural changes in the model food webs. Interestingly, food webs seem to be most sensitive to a random species loss after the loss of more than 25% of all initial species, suggesting that there is a threshold from which secondary extinctions increases. We also conclude that species being identified as keystones, based on the effect of their loss, are to some extent the same species being identified as having the largest effect on community structure and resilience, respectively, following a small perturbation.

Abstract [en]

Human-induced alterations in the birth and mortality rates of species and in the strength of interactions within and between species can lead to changes in the structure and resilience of ecological communities. Recent research points to the importance of considering the distribution of body sizes of species when exploring the response of communities to such perturbations. Here, we present a new size-based approach for assessing the sensitivity and elasticity of community structure (species equilibrium abundances) and resilience (rate of return to equilibrium) to changes in the intrinsic growth rate of species and in the strengths of species interactions. We apply this approach on two natural systems, the pelagic communities of the Baltic Sea and Lake Vättern, to illustrate how it can be used to identify potential keystone species and keystone links. We find that the keystone status of a species is closely linked to its body size. The analysis also suggests that communities are structurally and dynamically more sensitive to changes in the effects of prey on their consumers than in the effects of consumers on their prey. Moreover, we discuss how community sensitivity analysis can be used to study and compare the fragility of communities with different body size distributions by measuring the mean sensitivity or elasticity over all species or all interaction links in a community. We believe that the community sensitivity analysis developed here holds some promise for identifying species and links that are critical for the structural and dynamic robustness of ecological communities.

Ebenman, Bo

Abstract [en]

The majority of species in the ecosystems of the world are rare. Because the contributions to community biomass and productivity of many of these species are small it has been suggested that loss of rare species should have relatively small ecological consequences. However, the extent to which rare species affect the structure and stability of ecosystems is largely unknown. Using a theoretical approach, based on analytical methods, we here investigate how perturbations to rare as well as common species affect the structure (distribution of equilibrium abundances of species) and resilience (recovery rate) of complex ecological communities. We show that, contrary to expectation, resilience and structure of ecological communities are generally more sensitive to perturbations to rare than to common species. We find the explanation for this to lie in the cause of rarity: rare species tend to interact strongly, on a per capita basis, with other species. Our results suggest that many rare species are likely to fill important ecological roles in ecosystems.

Pimenov, Alexander

Palmer, Catherine

Environmental Research Institute, University College Cork, Cork, Ireland.

Emmerson, Mark

Environmental Research Institute, University College Cork, Cork, Ireland.

Jonsson, Tomas

Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden.

Show others...

(English)Manuscript (preprint) (Other academic)

Abstract [en]

Loss of species will directly change the structure of ecological communities, which in turn may cause additional species loss (secondary extinctions) due to indirect effects (e.g. loss of resources or altered population dynamics). The vulnerability of food webs to repeated species loss is expected to be affected by food web topology, species interactions and the order in which species go extinct. Species traits such as body size, abundance and connectivity probably determine the vulnerability to extinction of species and, thus, the order in which species go primarily extinct. However, how different sequences of primary extinctions affect the vulnerability of food webs to secondary extinctions, when species abundances are allowed to respond dynamically, is not well understood. So far, only one study has incorporated species dynamics when assessing the effect of different extinction sequences on community structure, and only a limited number of extinction sequences have been evaluated. Here, using complex model food webs and including population dynamics, we analyze the effect of 33 extinction sequences on community structure using R50 (the proportion of primarily removed species needed to cause a 50% reduction in species richness) as a measure of community robustness to secondary extinctions. As expected, we find community structure to be highly vulnerable to removal of primary producers. More surprisingly, removing species based on traits that are strongly linked to the trophic position of species (such as large-bodied species, rare species, species with a high net effect, species with a high trophic position) are found to be as destructive as removing only primary producers. Such top-down oriented removal of species are often considered to correspond to realistic primary extinctions of species, but earlier studies, based on topological approaches, have not found such realistic extinction sequences to have any drastic effect on the remaining community. Thus, our result suggests that ecological communities could be more vulnerable to realistic extinction sequences than previously believed.

Keywords

Community structure, extinction sequence, food webs, species loss, community robustness

Pimenov, Alexander

Palmer, Catherine

Environmental Research Institute, University College Cork, Cork, Ireland.

Emmerson, Mark

Environmental Research Institute, University College Cork, Cork, Ireland.

Jonsson, Tomas

Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden.

Show others...

(English)Manuscript (preprint) (Other academic)

Abstract [en]

Global change keeps pushing species towards extinction which results in altered structures of ecological communities. Consequently, the loss of certain species can trigger a cascade of secondary extinctions resulting in further degradation of the system. The importance of species for upholding the structure of communities may be linked to the traits of species. However, due to the altered structure of communities following species loss, the importance of species (and species traits) may change as the structure of the food web change. Using a dynamical approach and simulating species loss in complex model communities we analyze the potential importance of 11 species traits. We find that the most important trait varies for different degree of food web collapse and food web connectance. Though, as the most important traits of species usually are correlated we conclude that the importance of species traits is rather robust against structural changes in the communities (especially when only consumer species are targets of primarily extinctions). Interestingly, food webs display a collapse threshold (after the initial loss of approximately 25% of all species) from which secondary extinctions increases. Finally, consider only the loss of consumer species, the effect (number of secondary extinctions) on community structure caused by a large perturbation (species loss) is positively correlated to the response of food webs resulting from a small perturbation to the same species.

Keywords

Community structure, extinction sequence, food webs, species loss, community robustness

Human-induced alterations in the birth and mortality rates of species and in the strength of interactions within and between species can lead to changes in the structure and resilience of ecological communities. Recent research points to the importance of considering the distribution of body sizes of species when exploring the response of communities to such perturbations. Here, we present a new size-based approach for assessing the sensitivity and elasticity of community structure (species equilibrium abundances) and resilience (rate of return to equilibrium) to changes in the intrinsic growth rate of species and in the strengths of species interactions. We apply this approach on two natural systems, the pelagic communities of the Baltic Sea and Lake Vättern, to illustrate how it can be used to identify potential keystone species and keystone links. We find that the keystone status of a species is closely linked to its body size. The analysis also suggests that communities are structurally and dynamically more sensitive to changes in the effects of prey on their consumers than in the effects of consumers on their prey. Moreover, we discuss how community sensitivity analysis can be used to study and compare the fragility of communities with different body size distributions by measuring the mean sensitivity or elasticity over all species or all interaction links in a community. We believe that the community sensitivity analysis developed here holds some promise for identifying species and links that are critical for the structural and dynamic robustness of ecological communities.

The majority of species in the ecosystems of the world are rare. Because the contributions to community biomass and productivity of many of these species are small it has been suggested that loss of rare species should have relatively small ecological consequences. However, the extent to which rare species affect the structure and stability of ecosystems is largely unknown. Using a theoretical approach, based on analytical methods, we here investigate how perturbations to rare as well as common species affect the structure (distribution of equilibrium abundances of species) and resilience (recovery rate) of complex ecological communities. We show that, contrary to expectation, resilience and structure of ecological communities are generally more sensitive to perturbations to rare than to common species. We find the explanation for this to lie in the cause of rarity: rare species tend to interact strongly, on a per capita basis, with other species. Our results suggest that many rare species are likely to fill important ecological roles in ecosystems.

Loss of species will directly change the structure of ecological communities, which in turn may cause additional species loss (secondary extinctions) due to indirect effects (e.g. loss of resources or altered population dynamics). The vulnerability of food webs to repeated species loss is expected to be affected by food web topology, species interactions and the order in which species go extinct. Species traits such as body size, abundance and connectivity probably determine the vulnerability to extinction of species and, thus, the order in which species go primarily extinct. However, how different sequences of primary extinctions affect the vulnerability of food webs to secondary extinctions, when species abundances are allowed to respond dynamically, is not well understood. So far, only one study has incorporated species dynamics when assessing the effect of different extinction sequences on community structure, and only a limited number of extinction sequences have been evaluated. Here, using complex model food webs and including population dynamics, we analyze the effect of 33 extinction sequences on community structure using R50 (the proportion of primarily removed species needed to cause a 50% reduction in species richness) as a measure of community robustness to secondary extinctions. As expected, we find community structure to be highly vulnerable to removal of primary producers. More surprisingly, removing species based on traits that are strongly linked to the trophic position of species (such as large-bodied species, rare species, species with a high net effect, species with a high trophic position) are found to be as destructive as removing only primary producers. Such top-down oriented removal of species are often considered to correspond to realistic primary extinctions of species, but earlier studies, based on topological approaches, have not found such realistic extinction sequences to have any drastic effect on the remaining community. Thus, our result suggests that ecological communities could be more vulnerable to realistic extinction sequences than previously believed.

10.

Berg, Sofia

et al.

Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology. Linköping University, The Institute of Technology. University of Skovde, Sweden.

Pimenov, Alexander

Weierstrass Institute, Germany; National University of Ireland University of Coll Cork, Ireland.

Palmer, Catherine

Weierstrass Institute, Germany.

Emmerson, Mark

Queens University of Belfast, North Ireland.

Jonsson, Tomas

University of Skovde, Sweden; Swedish University of Agriculture Science, Sweden.

Loss of species will directly change the structure and potentially the dynamics of ecological communities, which in turn may lead to additional species loss (secondary extinctions) due to direct and/or indirect effects (e.g. loss of resources or altered population dynamics). Furthermore, the vulnerability of food webs to repeated species loss is expected to be affected by food web topology, species interactions, as well as the order in which species go extinct. Species traits such as body size, abundance and connectivity might determine a species vulnerability to extinction and, thus, the order in which species go primarily extinct. Yet, the sequence of primary extinctions, and their effects on the vulnerability of food webs to secondary extinctions, when species abundances are allowed to respond dynamically, has only recently become the focus of attention. Here, we analyse and compare topological and dynamical robustness to secondary extinctions of model food webs, in the face of 34 extinction sequences based on species traits. Although secondary extinctions are frequent in the dynamical approach and rare in the topological approach, topological and dynamical robustness tends to be correlated for many bottom-up directed, but not for top-down directed deletion sequences. Furthermore, removing species based on traits that are strongly positively correlated to the trophic position of species (such as large body size, low abundance, high net effect) is, under the dynamical approach, found to be as destructive as removing primary producers. Such top-down oriented removal of species are often considered to correspond to realistic extinction scenarios, but earlier studies, based on topological approaches, have found such extinction sequences to have only moderate effects on the remaining community. Thus, our result suggests that the structure of ecological communities, and therefore the integrity of important ecosystem processes could be more vulnerable to realistic extinction sequences than previously believed.

Global change keeps pushing species towards extinction which results in altered structures of ecological communities. Consequently, the loss of certain species can trigger a cascade of secondary extinctions resulting in further degradation of the system. The importance of species for upholding the structure of communities may be linked to the traits of species. However, due to the altered structure of communities following species loss, the importance of species (and species traits) may change as the structure of the food web change. Using a dynamical approach and simulating species loss in complex model communities we analyze the potential importance of 11 species traits. We find that the most important trait varies for different degree of food web collapse and food web connectance. Though, as the most important traits of species usually are correlated we conclude that the importance of species traits is rather robust against structural changes in the communities (especially when only consumer species are targets of primarily extinctions). Interestingly, food webs display a collapse threshold (after the initial loss of approximately 25% of all species) from which secondary extinctions increases. Finally, consider only the loss of consumer species, the effect (number of secondary extinctions) on community structure caused by a large perturbation (species loss) is positively correlated to the response of food webs resulting from a small perturbation to the same species.

12.

Berlow, E.L.

et al.

University of California, White Mountain Research Station, Bishop, CA 93514, United States, Department of Integrative Biology, University of California, Berkeley, CA 94720, United States.

1. Recent efforts to understand how the patterning of interaction strength affects both structure and dynamics in food webs have highlighted several obstacles to productive synthesis. Issues arise with respect to goals and driving questions, methods and approaches, and placing results in the context of broader ecological theory. 2. Much confusion stems from lack of clarity about whether the questions posed relate to community-level patterns or to species dynamics, and to what authors actually mean by the term 'interaction strength'. Here, we describe the various ways in which this term has been applied and discuss the implications of loose terminology and definition for the development of this field. 3. Of particular concern is the clear gap between theoretical and empirical investigations of interaction strengths and food web dynamics. The ecological community urgently needs to explore new ways to estimate biologically reasonable model coefficients from empirical data, such as foraging rates, body size, metabolic rate, biomass distribution and other species traits. 4. Combining numerical and analytical modelling approaches should allow exploration of the conditions under which different interaction strengths metrics are interchangeable with regard to relative magnitude, system responses, and species identity. 5. Finally, the prime focus on predator-prey links in much of the research to date on interaction strengths in food webs has meant that the potential significance of nontrophic interactions, such as competition, facilitation and biotic disturbance, has been largely ignored by the food web community. Such interactions may be important dynamically and should be routinely included in future food web research programmes.

Despite the fact that the loss of a species from a community has the potential to cause a dramatic decline in biodiversity, for example through cascades of secondary extinctions, little is known about the factors contributing to the extinction risk of any particular species. Here we expand earlier modeling approaches using a dynamic food-web model that accounts for bottom-up as well as top-down effects. We investigate what factors influence a species’ extinction risk and time to extinction of the non-persistent species. We identified three basic properties that affect a species’ risk of extinction. The highest extinction risk is born by species with (1) low energy input (e.g. high trophic level), (2) susceptibility to the loss of energy pathways (e.g. specialists with few prey species) and (3) dynamic instability (e.g. low Hill exponent and reliance on homogeneous energy channels when feeding on similarly sized prey). Interestingly, and different from field studies, we found that the trophic level and not the body mass of a species influences its extinction risk. On the other hand, body mass is the single most important factor determining the time to extinction of a species, resulting in small species dying first. This suggests that in the field the trophic level might have more influence on the extinction risk than presently recognized.

Warming and eutrophication are two of the most important global change stressors for natural ecosystems, but their interaction is poorly understood. We used a dynamic model of complex, size-structured food webs to assess interactive effects on diversity and network structure. We found antagonistic impacts: Warming increases diversity in eutrophic systems and decreases it in oligotrophic systems. These effects interact with the community size structure: Communities of similarly sized species such as parasitoid-host systems are stabilized by warming and destabilized by eutrophication, whereas the diversity of size-structured predator-prey networks decreases strongly with warming, but decreases only weakly with eutrophication. Nonrandom extinction risks for generalists and specialists lead to higher connectance in networks without size structure and lower connectance in size-structured communities. Overall, our results unravel interactive impacts of warming and eutrophication and suggest that size structure may serve as an important proxy for predicting the community sensitivity to these global change stressors.

Many of the earth’s ecosystems are experiencing large species losses due to human impacts such as habitat destruction and fragmentation, climate change, species invasions, pollution, and overfishing. Due to the complex interactions between species in food webs the extinction of one species could lead to a cascade of further extinctions and hence cause dramatic changes in species composition and ecosystem processes. The complexity of ecological systems makes it difficult to study them empirically. The systems often consist of large species numbers with lots of interactions between species. Investigating ecological communities within a theoretical approach, using mathematical models and computer simulations, is an alternative or a complement to experimental studies. This thesis is a collection of theoretical studies. We use model food webs in order to explore how biodiversity (species number) affects the response of communities to species loss (Paper I-III) and to environmental variability (Paper IV).

In paper I and II we investigate the risk of secondary extinctions following deletion of one species. It is shown that resistance against additional species extinctions increases with redundancy (number of species per functional group) (Paper I) in the absence of competition between basal species but decreases with redundancy in the presence of competition between basal species (Paper II). It is further shown that food webs with low redundancy run the risk of losing a greater proportion of species following a species deletion in a deterministic environment but when demographic stochasticity is included the benefits of redundancy are largely lost (Paper II). This finding implies that in the construction of nature reserves the advantages of redundancy for conservation of communities may be lost if the reserves are small in size. Additionally, food webs show higher risks of further extinctions after the loss of basal species and herbivores than after the loss of top predators (Paper I and II).

Secondary extinctions caused by a primary extinction and mediated through direct and indirect effects, are likely to occur with a time delay since the manifestation of indirect effects can take long time to appear. In paper III we show that the loss of a top predator leads to a significantly earlier onset of secondary extinctions in model communities than does the loss of a species from other trophic levels. If local secondary extinctions occur early they are less likely to be balanced by immigration of species from local communities nearby implying that secondary extinctions caused by the loss of top predators are less likely to be balanced by dispersal than secondary extinctions caused by the loss of other species. As top predators are vulnerable to human-induced disturbances on ecosystems in the first place, our results suggest that conservation of top predators should be a priority. Moreover, in most cases time to secondary extinction is shown to increase with species richness indicating the decay of ecological communities to be slower in species-rich than in species-poor communities.

Apart from the human-induced disturbances that often force species towards extinction the environment is also, to a smaller or larger extent, varying over time in a natural way. Such environmental stochasticity influences the dynamics of populations. In paper IV we compare the responses of food webs of different sizes to environmental stochasticity. Species-rich webs are found to be more sensitive to environmental stochasticity. Particularly, species-rich webs lose a greater proportion of species than species-poor webs and they also begin losing species faster than species-poor webs. However, once one species is lost time to final extinction is longer in species-rich webs than in species-poor webs. We also find that the results differ depending on whether species respond similarly to environmental fluctuations or whether they are totally uncorrelated in their response. For a given species richness, communities with uncorrelated species responses run a considerable higher risk of losing a fixed proportion of species compared with communities with correlated species responses.

Abstract [en]

Due to the complex interactions between species in food webs, the extinction of one species could lead to a cascade of further extinctions and hence cause dramatic changes in species composition and ecosystem processes. We found that the risk of additional species extinction, following the loss of one species in model food webs, decreases with the number of species per functional group. For a given number of species per functional group, the risk of further extinctions is highest when an autotroph is removed and lowest when a top predator is removed. In addition, stability decreases when the distribution of interaction strengths in the webs is changed from equal to skew (few strong and many weak links). We also found that omnivory appears to stabilize model food webs. Our results indicate that high biodiversity may serve as an insurance against radical ecosystem changes.

Abstract [en]

The loss of a species from an ecological community can set up a cascade of secondary extinctions that in the worst case could lead to the collapse of the community. Both deterministic and stochastic mechanisms may be involved in such secondary extinctions. To investigate the extent of secondary extinctions in ecological communities following the loss of a species, we here develop a community viability analysis. We introduce a measure called the “quasi-collapse risk” that is defined as the probability that the number of species in a community falls below some defined value within a fixed period of time following the loss of a species. We develop deterministic and stochastic methods for finding post-extinction communities. We use these methods to investigate the relationship between diversity (species richness) and quasi-collapse risks in model communities. It is shown that, in a deterministic context, communities with more species within trophic levels have a larger fraction of species remaining in post-extinction communities. This benefit of species richness is to a large extent lost in the presence of demographic stochasticity. The reason for this is a negative relationship between population density and species diversity. We also show that communities become increasingly triangular in shape as secondary extinctions take place, due to greater extinction risk of species at higher trophic levels. We argue that this new approach holds some promise for identifying fragile ecosystems and keystone species.

Abstract [en]

The large vulnerability of top predators to human-induced disturbances on ecosystems is a matter of growing concern. Because top predators often exert strong influence on their prey populations their extinction can have far-reaching consequences for the structure and functioning of ecosystems. It has, for example, been observed that the local loss of a predator can trigger a cascade of secondary extinctions. However, the time lags involved in such secondary extinctions remain unexplored. Here we show that the loss of a top predator leads to a significantly earlier onset of secondary extinctions in model communities than does the loss of a species from other trophic levels. Moreover, in most cases time to secondary extinction increases with increasing species richness. If local secondary extinctions occur early they are less likely to be balanced by immigration of species from local communities nearby. The implications of these results for community persistence and conservation priorities are discussed.

The large vulnerability of top predators to human-induced disturbances on ecosystems is a matter of growing concern. Because top predators often exert strong influence on their prey populations their extinction can have far-reaching consequences for the structure and functioning of ecosystems. It has, for example, been observed that the local loss of a predator can trigger a cascade of secondary extinctions. However, the time lags involved in such secondary extinctions remain unexplored. Here we show that the loss of a top predator leads to a significantly earlier onset of secondary extinctions in model communities than does the loss of a species from other trophic levels. Moreover, in most cases time to secondary extinction increases with increasing species richness. If local secondary extinctions occur early they are less likely to be balanced by immigration of species from local communities nearby. The implications of these results for community persistence and conservation priorities are discussed.

Due to the complex interactions between species in food webs, the extinction of one species could lead to a cascade of further extinctions and hence cause dramatic changes in species composition and ecosystem processes. We found that the risk of additional species extinction, following the loss of one species in model food webs, decreases with the number of species per functional group. For a given number of species per functional group, the risk of further extinctions is highest when an autotroph is removed and lowest when a top predator is removed. In addition, stability decreases when the distribution of interaction strengths in the webs is changed from equal to skew (few strong and many weak links). We also found that omnivory appears to stabilize model food webs. Our results indicate that high biodiversity may serve as an insurance against radical ecosystem changes.

The structure of contacts that mediate transmission has a pronounced effect on the outbreak dynamics of infectious disease and simulation models are powerful tools to inform policy decisions. Most simulation models of livestock disease spread rely to some degree on predictions of animal movement between holdings. Typically, movements are more common between nearby farms than between those located far away from each other. Here, we assessed spatiotemporal variation in such distance dependence of animal movement contacts from an epidemiological perspective. We evaluated and compared nine statistical models, applied to Swedish movement data from 2008. The models differed in at what level ( if at all), they accounted for regional and/or seasonal heterogeneities in the distance dependence of the contacts. Using a kernel approach to describe how probability of contacts between farms changes with distance, we developed a hierarchical Bayesian framework and estimated parameters by using Markov Chain Monte Carlo techniques. We evaluated models by three different approaches of model selection. First, we used Deviance Information Criterion to evaluate their performance relative to each other. Secondly, we estimated the log predictive posterior distribution, this was also used to evaluate their relative performance. Thirdly, we performed posterior predictive checks by simulating movements with each of the parameterized models and evaluated their ability to recapture relevant summary statistics. Independent of selection criteria, we found that accounting for regional heterogeneity improved model accuracy. We also found that accounting for seasonal heterogeneity was beneficial, in terms of model accuracy, according to two of three methods used for model selection. Our results have important implications for livestock disease spread models where movement is an important risk factor for between farm transmission. We argue that modelers should refrain from using methods to simulate animal movements that assume the same pattern across all regions and seasons without explicitly testing for spatiotemporal variation.

Understanding the consequences of species loss in complex ecological communities is one of the great challenges in current biodiversity research. For a long time, this topic has been addressed by traditional biodiversity experiments. Most of these approaches treat species as trait-free, taxonomic units characterizing communities only by species number without accounting for species traits. However, extinctions do not occur at random as there is a clear correlation between extinction risk and species traits. In this review, we assume that large species will be most threatened by extinction and use novel allometric and size-spectrum concepts that include body mass as a primary species trait at the levels of populations and individuals, respectively, to re-assess three classic debates on the relationships between biodiversity and (i) food-web structural complexity, (ii) community dynamic stability, and (iii) ecosystem functioning. Contrasting current expectations, size-structured approaches suggest that the loss of large species, that typically exploit most resource species, may lead to future food webs that are less interwoven and more structured by chains of interactions and compartments. The disruption of natural body-mass distributions maintaining food-web stability may trigger avalanches of secondary extinctions and strong trophic cascades with expected knock-on effects on the functionality of the ecosystems. Therefore, we argue that it is crucial to take into account body size as a species trait when analysing the consequences of biodiversity loss for natural ecosystems. Applying size-structured approaches provides an integrative ecological concept that enables a better understanding of each species' unique role across communities and the causes and consequences of biodiversity loss.

Aspects of spatial scale have until recently been largely ignored in empirical and theoretical food web studies (e.g., Cohen & Briand 1984, Martinez 1992, but see Bengtsson et al. 2002, Bengtsson & Berg, this book). Most ecologists tend to conceptualize and represent food webs as static representations of communities, depicting a community assemblage as sampled at a particular point in time, or highly aggregated trophic group composites over broader scales of time and space (Polis et al. 1996). Moreover, most researchers depict potential food webs, which contain all species sampled and all potential trophic links based on literature reviews, several sampling events, or laboratory feeding trials. In reality, however, not all these potential feeding links are realized as not all species co-occur, and not all samples in space or time can contain all species (Schoenly & Cohen 1991), hence, yielding a variance of food web architecture in space (Brose et al. 2004). In recent years, food web ecologists have recognized that food webs are open systems – that are influence by processes in adjacent systems – and spatially heterogeneous (Polis et al. 1996). This influence of adjacent systems can be bottom-up, due to allochthonous inputs of resources (Polis & Strong 1996, Huxel & McCann 1998, Mulder & De Zwart 2003), or top-down due to the regular or irregular presence of top predators (e.g., Post et al. 2000, Scheu 2001). However, without a clear understanding of the size of a system and a definition of its boundaries it is not possible to judge if flows are internal or driven by adjacent systems. Similarly, the importance of allochthony is only assessable when the balance of inputs and outputs are known relative to the scale and throughputs within the system itself. At the largest scale of the food web – the home range of a predator such as wolf, lion, shark or eagle of roughly 50 km2 to 300 km2 –the balance of inputs and outputs caused by wind and movement of water may be small compared to the total trophic flows within the home range of the large predator (Cousins 1990). Acknowledging these issues of space, Polis et al (1996) argued that progress toward the next phase of food web studies would require addressing spatial and temporal processes. Here, we present a conceptual framework with some nuclei about the role of space in food web ecology. Although we primarily address spatial aspects, this framework is linked to a more general concept of spatio-temporal scales of ecological research.

Globalization has increased the potential for the introduction and spread of novel pathogens over large spatial scales necessitating continental-scale disease models to guide emergency preparedness. Livestock disease spread models, such as those for the 2001 foot-and-mouth disease (FMD) epidemic in the United Kingdom, represent some of the best case studies of large-scale disease spread. However, generalization of these models to explore disease outcomes in other systems, such as the United Statess cattle industry, has been hampered by differences in system size and complexity and the absence of suitable livestock movement data. Here, a unique database of US cattle shipments allows estimation of synthetic movement networks that inform a near-continental scale disease model of a potential FMD-like (i.e., rapidly spreading) epidemic in US cattle. The largest epidemics may affect over one-third of the US and 120,000 cattle premises, but cattle movement restrictions from infected counties, as opposed to national movement moratoriums, are found to effectively contain outbreaks. Slow detection or weak compliance may necessitate more severe state-level bans for similar control. Such results highlight the role of large-scale disease models in emergency preparedness, particularly for systems lacking comprehensive movement and outbreak data, and the need to rapidly implement multi-scale contingency plans during a potential US outbreak.

Ecological communities are continuously exposed to natural or anthropogenic disturbances of varied intensity and frequency. The way communities respond to disturbances can depend on various factors, such as number of species, structural characteristics of the community, stability properties, species characteristics and the nature of the disturbance. This thesis is a collection of theoretical studies on how ecological communities respond to different kind of disturbances, mainly in relation to interaction strength between species, a measure of how strongly or weakly species interact with each other.

A major disturbance for natural communities is the loss of a species. Although species extinctions is a natural process in the geological time scale, it has lately been dangerously accelerated due to human activities and interferences. Extinction of a species can have dramatic consequences for the community, can trigger a cascade of secondary species extinction and can even lead to community collapse. In Paper I, we identify species whose loss can trigger a large number of secondary extinctions (namely keystone species), species that are particularly vulnerable to become extinct following the loss of another species and mechanisms behind the sequence of secondary extinctions. We also highlight the fact that the keystone status of a species can be context dependent, that is, it is dependent on the structure of the community where it is embedded.

Although the global extinction of a species is an irreversible process, in cases of local extinction, conservation and restoration plans can include reintroduction of the species to their former location. Such reintroduction or translocation attempts often fail, due to characteristics of the reintroduced species and to changes in the community structure caused by the initial loss of the species (Paper II ). Using model communities we show that this risk of reintroduction failure can be high - even in cases where the initial species loss did not cause any secondary extinctions - and it differs between attempts to reintroduce weakly or strongly interacting species (Paper II ).

Disturbances are not always as profound as species extinction. Human activities and environmental changes can cause small and permanent changes in birth and mortality rates of species and in the strength of interaction between species. Such disturbances can change the stability properties of ecological communities making them more vulnerable to further disturbances. In Paper III, we derive analytical expressions for the sensitivity of resilience to changes in the intrinsic growth rate of species and in the strength of interaction links. We also apply the method to model communities and identify keystone species and links, i.e. species and links whose small disturbance would cause large changes in community resilience. We found that changes in the growth rate of strongly interacting species have a larger impact on resilience than changes in the growth rate of weakly interacting species, which is in line with the main findings of the species deletion study (Paper I ).

Community complexity - mainly expressed as number of species and links - was one of the first community characteristics to be related to stability properties and the way communities respond to disturbances. Many theoretical works support the hypothesis that complexity reduces stability, contradicting intuition, observation and many experimental studies. In Paper IV, we state that this could be, at least partly, due to methodological misconceptions and misinterpretations. We propose a new sampling method for parameterizing model communities and we highlight the importance of feasibility of model communities (all species densities are strictly positive), for a more proper estimation of stability probability of communities with different degrees of complexity.

Abstract [en]

The loss of a species from an ecological community can trigger a cascade of secondary extinctions. The probability of secondary extinction to take place and the number of secondary extinctions are likely to depend on the characteristics of the species that is lost—the strength of its interactions with other species—as well as on the distribution of interaction strengths in the whole community. Analysing the effects of species loss in model communities we found that removal of the following species categories triggered, on average, the largest number of secondary extinctions: (a) rare species interacting strongly with many consumers, (b) abundant basal species interacting weakly with their consumers and (c) abundant intermediate species interacting strongly with many resources. We also found that the keystone status of a species with given characteristics was context dependent, that is, dependent on the structure of the community where it was embedded. Species vulnerable to secondary extinctions were mainly species interacting weakly with their resources and species interacting strongly with their consumers.

Ebenman, Bo

Abstract [en]

For many threatened species reintroduction of captive-reared individuals into the wild may offer the only hope of preventing global extinction. However, attempts to reintroduce a species into an ecological community from which it has once gone extinct often fail. This can be due to captivity-induced genetic and behavioural changes in the species itself. Here we argue that also changes in the structure of the community caused by the initial loss of the species can hinder its subsequent reintroduction. Due to the interdependences amongspecies in ecological communities the local extinction of a species leads to changes in the densities and strength of interactions among the remaining species in the community and sometimes even to a cascade of secondary extinctions. Such alterations in the structure of a community caused by the initial extinction of the species might make it impossible for the species to reinvade at a later stage. Here we show, using models of multitrophic communities, that the risk of reintroduction failure can be high and that it differs between species belonging to different trophic levels and between weakly and strongly interacting species. Specifically, there is a high risk of reintroduction failure for primary producer species and weakly interacting consumer species. We also find the risk that the reintroduction will cause new extinctions to be higher in communities where the initial loss triggered secondary extinctions. In the worst case extinctions caused by the reintroduction may lead to the subsequent extinction of the reintroduced species itself. This risk is not negligible implicating that reintroductions might sometimes aggravate the state of local communities.

Ebenman, Bo

Abstract [en]

Human-induced changes in the birth and mortality rates of species and in the strength of interactions within and between species can lead to changes in the resilience of ecological communities. Here we derive analytical expressions for the sensitivity of community resilience to changes in the intrinsic growth rate of species and in the strengths of interaction links. These new methods are applied on model communities to illustrate how they can be used to identify keystone species and keystone links - keystone species and keystone links in the sensethat small changes in their growth rates and strengths, respectively, will have large effects on the resilience of the community. We find that small changes in the intrinsic growth rates of rare species (e.g. top predators) and strongly interacting species have larger effect on resilience than changes in the growth rates of abundant species and weakly interacting species. Moreover, we find that small changes in the strength of weak interaction links cause larger changes in resilience than changes in the strength of strong links. We believe that thecommunity sensitivity analysis developed here holds some promise for identifying species and links that are critical for the resilience of ecological communities.

Christianou, Maria

Kokkoris, Giorgos D.

Dept. of Marine Sciences, Faculty of Environment, University of the Aegean, Mytilene, Lesvos Island, Greece.

(English)Manuscript (Other academic)

Abstract [en]

The complexity - stability relation has been a central issue in ecology for a long time. Both theoretical and empirical studies have been investigating whether complexity promotes stability or not, which could be the underlying mechanisms creating a positive or negative cmnplexity-stability relation and which are the structures, characteristics and constraints that would allow complex ecological systems to persist and be stable. In this paper we approach the subject from amethodological point of view. We study the effect of parameterizing the communities in a certain way and illustrate the effect of treating feasibility (i.e. densities of all species are strictly positive) separately from stability. We observe that increasing number of species in the communities requires a more skewed interaction strength distribution toward weak interactions, in order for the communities to theoretically exist. Using model Lotka-Volterra competition communities we illustrate that probability of feasibility decreases with increasing interaction strength and number of species in the community. However, forfeasible systems we find that local stability probability and resilience do not significantly differ between communities with few or many species, in contrast with earlier studies that, did not account for feasibility and concluded that species poor communities had higher probability of being locally stable than species rich communities.

The loss of a species from an ecological community can trigger a cascade of secondary extinctions. The probability of secondary extinction to take place and the number of secondary extinctions are likely to depend on the characteristics of the species that is lost—the strength of its interactions with other species—as well as on the distribution of interaction strengths in the whole community. Analysing the effects of species loss in model communities we found that removal of the following species categories triggered, on average, the largest number of secondary extinctions: (a) rare species interacting strongly with many consumers, (b) abundant basal species interacting weakly with their consumers and (c) abundant intermediate species interacting strongly with many resources. We also found that the keystone status of a species with given characteristics was context dependent, that is, dependent on the structure of the community where it was embedded. Species vulnerable to secondary extinctions were mainly species interacting weakly with their resources and species interacting strongly with their consumers.

For many threatened species reintroduction of captive-reared individuals into the wild may offer the only hope of preventing global extinction. However, attempts to reintroduce a species into an ecological community from which it has once gone extinct often fail. This can be due to captivity-induced genetic and behavioural changes in the species itself. Here we argue that also changes in the structure of the community caused by the initial loss of the species can hinder its subsequent reintroduction. Due to the interdependences amongspecies in ecological communities the local extinction of a species leads to changes in the densities and strength of interactions among the remaining species in the community and sometimes even to a cascade of secondary extinctions. Such alterations in the structure of a community caused by the initial extinction of the species might make it impossible for the species to reinvade at a later stage. Here we show, using models of multitrophic communities, that the risk of reintroduction failure can be high and that it differs between species belonging to different trophic levels and between weakly and strongly interacting species. Specifically, there is a high risk of reintroduction failure for primary producer species and weakly interacting consumer species. We also find the risk that the reintroduction will cause new extinctions to be higher in communities where the initial loss triggered secondary extinctions. In the worst case extinctions caused by the reintroduction may lead to the subsequent extinction of the reintroduced species itself. This risk is not negligible implicating that reintroductions might sometimes aggravate the state of local communities.

Human-induced changes in the birth and mortality rates of species and in the strength of interactions within and between species can lead to changes in the resilience of ecological communities. Here we derive analytical expressions for the sensitivity of community resilience to changes in the intrinsic growth rate of species and in the strengths of interaction links. These new methods are applied on model communities to illustrate how they can be used to identify keystone species and keystone links - keystone species and keystone links in the sensethat small changes in their growth rates and strengths, respectively, will have large effects on the resilience of the community. We find that small changes in the intrinsic growth rates of rare species (e.g. top predators) and strongly interacting species have larger effect on resilience than changes in the growth rates of abundant species and weakly interacting species. Moreover, we find that small changes in the strength of weak interaction links cause larger changes in resilience than changes in the strength of strong links. We believe that thecommunity sensitivity analysis developed here holds some promise for identifying species and links that are critical for the resilience of ecological communities.

The complexity - stability relation has been a central issue in ecology for a long time. Both theoretical and empirical studies have been investigating whether complexity promotes stability or not, which could be the underlying mechanisms creating a positive or negative cmnplexity-stability relation and which are the structures, characteristics and constraints that would allow complex ecological systems to persist and be stable. In this paper we approach the subject from amethodological point of view. We study the effect of parameterizing the communities in a certain way and illustrate the effect of treating feasibility (i.e. densities of all species are strictly positive) separately from stability. We observe that increasing number of species in the communities requires a more skewed interaction strength distribution toward weak interactions, in order for the communities to theoretically exist. Using model Lotka-Volterra competition communities we illustrate that probability of feasibility decreases with increasing interaction strength and number of species in the community. However, forfeasible systems we find that local stability probability and resilience do not significantly differ between communities with few or many species, in contrast with earlier studies that, did not account for feasibility and concluded that species poor communities had higher probability of being locally stable than species rich communities.

Many different concepts have been used to describe species' roles in food webs (i.e., the ways in which species participate in their communities as consumers and resources). As each concept focuses on a different aspect of food-web structure, it can be difficult to relate these concepts to each other and to other aspects of ecology. Here we use the Eltonian niche as an overarching framework, within which we summarize several commonly-used role concepts (degree, trophic level, motif roles, and centrality). We focus mainly on the topological versions of these concepts but, where dynamical versions of a role concept exist, we acknowledge these as well. Our aim is to highlight areas of overlap and ambiguity between different role concepts and to describe how these roles can be used to group species according to different strategies (i.e., equivalence and functional roles). The existence of “gray areas” between role concepts make it essential for authors to carefully consider both which role concept(s) are most appropriate for the analyses they wish to conduct and what aspect of species' niches (if any) they wish to address. The ecological meaning of differences between species' roles can change dramatically depending on which role concept(s) are used.

Food webs and meso-scale motifs allow us to understand the structure of ecological communities and define species roles within them. This species-level perspective on networks permits tests for relationships between species traits and their patterns of direct and indirect interactions. Such relationships could allow us to predict food-web structure based on more easily obtained trait information. Here, we calculated the roles of species (as vectors of motif position frequencies) in six well-resolved marine food webs and identified the motif positions associated with the greatest variation in species roles. We then tested whether the frequencies of these positions varied with species traits. Despite the coarse-grained traits we used, our approach identified several strong associations between traits and motifs. Feeding environment was a key trait in our models and may shape species roles by affecting encounter probabilities. Incorporating environment into future food-web models may improve predictions of an unknown network structure.

Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology. Linköping University, Faculty of Science & Engineering. University of Canterbury, New Zealand; University of Otago, New Zealand.

Some parasites move from one host to another via trophic transmission, the consumption of the parasite (inside its current host) by its future host. Feeding links among free-living species can thus be understood as potential transmission routes for parasites. As these links have different dynamic and structural properties, they may also vary in their effectiveness as trophic transmission routes. That is, some links may be better than others in allowing parasites to complete their complex life cycles. However, not all links are accessible to parasites as most are restricted to a small number of host taxa. This restriction means that differences between links involving host and non-host taxa must be considered when assessing whether transmission routes for parasites have different food web properties than other links. Here we use four New Zealand lake food webs to test whether link properties (contribution of a link to the predators diet, prey abundance, prey biomass, amount of biomass transferred, centrality, and asymmetry) affect trophic transmission of parasites. Critically, we do this using both models that neglect the taxonomy of free-living species and models that explicitly include information about which free-living species are members of suitable host taxa. Although the best-fit model excluding taxonomic information suggested that transmission routes have different properties than other feeding links, when including taxonomy, the best-fit model included only an intercept. This means that the taxonomy of free-living species is a key determinant of parasite transmission routes and that food-web properties of transmission routes are constrained by the properties of host taxa. In particular, many intermediate hosts (prey) attain high biomasses and are involved in highly central links while links connecting intermediate to definitive (predator) hosts tend to be dynamically weak.

Inter-annual turnover in community composition can affect the richness and functioning of ecological communities. If incoming and outgoing species do not interact with the same partners, ecological functions such as pollination may be disrupted. Here, we explore the extent to which turnover affects species' roles - as defined based on their participation in different motifs positions - in a series of temporally replicated plant-pollinator networks from high-Arctic Zackenberg, Greenland. We observed substantial turnover in the plant and pollinator assemblages, combined with significant variation in species' roles between networks. Variation in the roles of plants and pollinators tended to increase with the amount of community turnover, although a negative interaction between turnover in the plant and pollinator assemblages complicated this trend for the roles of pollinators. This suggests that increasing turnover in the future will result in changes to the roles of plants and likely those of pollinators. These changing roles may in turn affect the functioning or stability of this pollination network.

As an essential input to crop growth via soil reserves or fertilizer, phosphorus underpins global food security. Without phosphorus, food could not be produced, yet phosphorus is mined from fi nite reserves, most of which are controlled by only a few countries1 (UNEP 2011; Jasinski 2015; Cordell and White 2014). Fertilizer prices are likely to increase as fi nite reserves become critically scarce. Globally, a billion farmers and their families cannot access fertilizer markets and many rely on phosphorus-defi cient soils that produce low crop yields (IFPRI 2003). Moreover, mismanagement along the phosphorus supply chain from mine to fi eld to fork has resulted in massive losses and waste, which largely ends up in waterways, causing nutrient pollution and algal blooms (Bennett, Carpenter and Caraco 2001). The global phosphorus challenge is inherently complex; it is as much about international relations as farm soil fertility. It transcends disciplines, sectors, and scales – from geopolitics to ecology to nutrition. In this chapter, we describe and refl ect upon a new project using a novel transdisciplinary approach to address this phosphorus challenge.

In the dawning of what may become Earth’s 6th mass extinction the topic of this thesis, understanding extinction processes and what determines the magnitude of species loss, has become only too relevant. The number of known extinctions (~850) during the last centuries translates to extinction rates elevated above the background rate, matching those of previous mass extinction events. The main drivers of these extinctions have been human land use, introduction of exotic species and overexploitation. Under continued anthropogenic pressure and climate change, the current extinction rates are predicted to increase tenfold.

Large perturbations, such as the extinction drivers mentioned above, affects species directly, causing a change in their abundance. As species are not isolated, but connected to each other through a multitude of interactions, the change in abundance of one species can in turn affect others. Thus, in addition to the direct effect, a perturbation can affect a species indirectly through the ecological network in which the species is embedded. With this thesis, I wish to contribute to our basic understanding of these indirect effects and the role they play in determining the magnitude of species loss. All the studies included here are so called in silico experiments, using mathematical models to describe ecological communities and computer simulations to observe the response of these communities to perturbation.

When a perturbation is severe enough, a species will be driven to extinction. The loss of a species from a system is in itself a large perturbation, and may result in further extinctions, so called secondary extinctions. The traits of the species initially lost, can be a potential predictor of the magnitude of secondary species loss. In Paper I of this thesis, I show that when making such predictions, it is important to incorporate temporally dynamic species interactions and abundances, in order not to underestimate the importance of certain species, such as top predators.

I further show that species traits alone are not particularly good predictors of secondary extinction risk (Paper I), but that in combination with community level properties they are (Paper II). Indeed, there seems to be an interaction such that the specific property making a community prone to secondary species loss, depends on what kind of species was lost in the primary extinction. As different types of perturbation put different types of species at risk of (primary) extinction, this means that the specific property making a community prone to secondary species loss, will depend on the type of perturbation the community is subjected to.

One of the predicted main drivers of future species extinction is climate change. If the local climate becomes adverse, a species can either migrate to new and better areas or stay and evolve. Both these processes will be important in determining the magnitude of species loss under climate change. However, migration and evolution do not occur in vacuum – the biotic community in which these processes play out may modulate their effect on biodiversity. In paper III, I show that the strength of competition between species modulates the effect of both dispersal and evolution on the magnitude of species loss under climate change. The three-way interaction between interspecific competition, evolution and dispersal, creates a complex pattern of biodiversity responses, in which both evolution and dispersal can either increase or decrease the magnitude of species loss. Thus, when species interactions are incorporated, it is clear that even though migration and evolution may alleviate the impact of climate change for some species, they may indirectly aggravate the situation for others.

In Paper III, the aspect of climate change incorporated in the model is an increase in mean annual temperature. But climate change is also predicted to increase environmental variability. Paper IV shows that species-rich communities are more sensitive to high environmental variability than species-poor ones. The smaller population sizes in the species-rich communities increased the extinction risk connected to population fluctuations driven by the variable environment. Hence, systems such as tropical forests and coral reefs are predicted to be particularly sensitive to the increased variability that may follow with climate change.

In Paper IV, primary extinctions of primary producers result in extinction cascades of consumer species, when they lose their prey. However, in reality a consumer species might be able to switch to another prey, and such flexibility has both been observed and suggested as a potential rescue mechanism. But what is beneficial for an individual predator in the short-term can become detrimental to the ecological community in the long-term. Paper V shows that consumer flexibility often led to consumers continuously overexploiting their new prey, in the worst case to the point of system collapse. Thus, the suggested rescue mechanism aggravated the effect of initial species loss, rather than ameliorating it.

Overall, the research presented here, underscores the importance of including population dynamics and biotic interactions when studying the effects of perturbation on biodiversity. Many of the results are complex, hard to foresee or even counter-intuitive, arising from the indirect effects of the perturbation being translated through the living web of species interactions.

Abstract [en]

The loss of species from ecological communities can unleash a cascade of secondary extinctions, the risk and extent of which are likely to depend on the traits of the species that are lost from the community. To identify species traits that have the greatest impact on food web robustness to species loss we here subject allometrically scaled, dynamical food web models to several deletion sequences based on species’ connectivity, generality, vulnerability or body mass. Further, to evaluate the relative importance of dynamical to topological effects we compare robustness between dynamical and purely topological models. This comparison reveals that the topological approach overestimates robustness in general and for certain sequences in particular. Top-down directed sequences have no or very low impact on robustness in topological analyses, while the dynamical analysis reveals that they may be as important as high-impact bottom-up directed sequences. Moreover, there are no deletion sequences that result, on average, in no or very few secondary extinctions in the dynamical approach. Instead, the least detrimental sequence in the dynamical approach yields an average robustness similar to the most detrimental (non-basal) deletion sequence in the topological approach. Hence, a topological analysis may lead to erroneous conclusions concerning both the relative and the absolute importance of different species traits for robustness. The dynamical sequential deletion analysis shows that food webs are least robust to the loss of species that have many trophic links or that occupy low trophic levels. In contrast to previous studies we can infer, albeit indirectly, that secondary extinctions were triggered by both bottom-up and top-down cascades.

Ebenman, Bo

Abstract [en]

The ability to identify the ecosystems most vulnerable to species loss is fundamental for the allocation of conservation efforts. With this aim, the traits of keystone species have been investigated, as have the properties defining systems especially sensitive to species loss. However, these two have rarely been investigated in relation to each other. Here we show, that the traits of the species primarily lost act in conjunction with the properties of the food web from which it is lost, in determining the resistance of the system. We find that the extent of bottom-up extinction cascades is determined mainly by traits related to food web topology, while traits related to population dynamics govern the extent of top-down cascades. As different disturbances affect species with different traits, this interaction implies that the characteristics defining a sensitive community depend on the disturbance it is subjected to.

Abstract [en]

Climate change is predicted to have major implications for global biodiversity. Dispersal and evolution may become crucial for species survival, as species must either adapt or migrate to track the changing climate. However, migration and evolution do not occur in vacuum – the biotic community in which these processes play out may modulate their effect on biodiversity. Here, we use an eco-evolutionary, spatially explicit, multi-species model that allows us to examine the interactive effects of competition, adaptation and dispersal on species richness in plant communities under global warming. We find that there is a larger decline in global species richness when interspecific competition is strong. Furthermore, there is a three-way interaction between interspecific competition, evolution and dispersal that creates a complex pattern of biodiversity responses, in which both evolution and dispersal can either increase or decrease the magnitude of species loss. This interaction arises for at least two reasons: 1) different levels of dispersal, evolution and competition creates differences in local and global community structure before climate change, and 2) competitive interactions determine whether the benefits of dispersal and/or evolution (climate tracking and adaptation) outweighs the risks (competitive exclusion).

Abstract [en]

Global warming leads to increased intensity and frequency of weather extremes. Such increased environmental variability might in turn result in increased variation in the demographic rates of interacting species with potentially important consequences for the dynamics of food-webs. Using a theoretical approach we here explore the response of food-webs to a highly variable environment. We investigate how species richness and correlation in the responses of species to environmental fluctuations affect the risk of extinction cascades. We find that the risk of extinction cascades increases with increasing species richness, especially when correlation among species is low. Initial extinctions of primary producer species unleash bottom-up extinction cascades, especially in webs with specialist consumers. In this sense, species-rich ecosystems are less robust to increasing levels of environmental variability than species-poor ones. Our study thus suggests that highly species-rich ecosystems like coral reefs and tropical rainforests might be particularly vulnerable to increased climate variability.

Abstract [en]

Loss of one species in an ecosystem can trigger extinctions of other dependent species. For instance, specialist predators will go extinct following the loss of their only prey unless they can change their diet. It has therefore been suggested that an ability of consumers to rewire to novel prey should mitigate the consequences of species loss by reducing the risk of cascading extinction. Using a new modelling approach on natural and computer-generated food webs we find that, on the contrary, rewiring often aggravates the effects of species loss. This is because rewiring can lead to overexploitation of resources, which eventually causes extinction cascades. Such a scenario is particularly likely if prey species cannot escape predation when rare and if predators are efficient in exploiting novel prey. Indeed, rewiring is a two-edged sword; it might be advantageous for individual predators in the short term, yet harmful for long-term system persistence.

The loss of species from ecological communities can unleash a cascade of secondary extinctions, the risk and extent of which are likely to depend on the traits of the species that are lost from the community. To identify species traits that have the greatest impact on food web robustness to species loss we here subject allometrically scaled, dynamical food web models to several deletion sequences based on species’ connectivity, generality, vulnerability or body mass. Further, to evaluate the relative importance of dynamical to topological effects we compare robustness between dynamical and purely topological models. This comparison reveals that the topological approach overestimates robustness in general and for certain sequences in particular. Top-down directed sequences have no or very low impact on robustness in topological analyses, while the dynamical analysis reveals that they may be as important as high-impact bottom-up directed sequences. Moreover, there are no deletion sequences that result, on average, in no or very few secondary extinctions in the dynamical approach. Instead, the least detrimental sequence in the dynamical approach yields an average robustness similar to the most detrimental (non-basal) deletion sequence in the topological approach. Hence, a topological analysis may lead to erroneous conclusions concerning both the relative and the absolute importance of different species traits for robustness. The dynamical sequential deletion analysis shows that food webs are least robust to the loss of species that have many trophic links or that occupy low trophic levels. In contrast to previous studies we can infer, albeit indirectly, that secondary extinctions were triggered by both bottom-up and top-down cascades.

The ability to identify the ecosystems most vulnerable to species loss is fundamental for the allocation of conservation efforts. With this aim, the traits of keystone species have been investigated, as have the properties defining systems especially sensitive to species loss. However, these two have rarely been investigated in relation to each other. Here we show, that the traits of the species primarily lost act in conjunction with the properties of the food web from which it is lost, in determining the resistance of the system. We find that the extent of bottom-up extinction cascades is determined mainly by traits related to food web topology, while traits related to population dynamics govern the extent of top-down cascades. As different disturbances affect species with different traits, this interaction implies that the characteristics defining a sensitive community depend on the disturbance it is subjected to.

Climate change is predicted to have major implications for global biodiversity. Dispersal and evolution may become crucial for species survival, as species must either adapt or migrate to track the changing climate. However, migration and evolution do not occur in vacuum – the biotic community in which these processes play out may modulate their effect on biodiversity. Here, we use an eco-evolutionary, spatially explicit, multi-species model that allows us to examine the interactive effects of competition, adaptation and dispersal on species richness in plant communities under global warming. We find that there is a larger decline in global species richness when interspecific competition is strong. Furthermore, there is a three-way interaction between interspecific competition, evolution and dispersal that creates a complex pattern of biodiversity responses, in which both evolution and dispersal can either increase or decrease the magnitude of species loss. This interaction arises for at least two reasons: 1) different levels of dispersal, evolution and competition creates differences in local and global community structure before climate change, and 2) competitive interactions determine whether the benefits of dispersal and/or evolution (climate tracking and adaptation) outweighs the risks (competitive exclusion).

Managing ecosystems to provide ecosystem services in the face of global change is a pressing challenge for policy and science. Predicting how alternative management actions and changing future conditions will alter services is complicated by interactions among components in ecological and socioeconomic systems. Failure to understand those interactions can lead to detrimental outcomes from management decisions. Network theory that integrates ecological and socioeconomic systems may provide a path to meeting this challenge. While network theory offers promising approaches to examine ecosystem services, few studies have identified how to operationalize networks for managing and assessing diverse ecosystem services. We propose a framework for how to use networks to assess how drivers and management actions will directly and indirectly alter ecosystem services.

Food web topologies depict the community structure as distributions of feeding interactions across populations. Although the soil ecosystem provides important functions for aboveground ecosystems, data on complex soil food webs is notoriously scarce, most likely due to the difficulty of sampling and characterizing the system. To fill this gap we assembled the complex food webs of 48 forest soil communities. The food webs comprise 89 to 168 taxa and 729 to 3344 feeding interactions. The feeding links were established by combining several molecular methods (stable isotope, fatty acid and molecular gut content analyses) with feeding trials and literature data. First, we addressed whether soil food webs (n = 48) differ significantly from those of other ecosystem types (aquatic and terrestrial aboveground, n = 77) by comparing 22 food web parameters. We found that our soil food webs are characterized by many omnivorous and cannibalistic species, more trophic chains and intraguild-predation motifs than other food webs and high average and maximum trophic levels. Despite this, we also found that soil food webs have a similar connectance as other ecosystems, but interestingly a higher link density and clustering coefficient. These differences in network structure to other ecosystem types may be a result of ecosystem specific constraints on hunting and feeding characteristics of the species that emerge as network parameters at the food-web level. In a second analysis of land-use effects, we found significant but only small differences of soil food web structure between different beech and coniferous forest types, which may be explained by generally strong selection effects of the soil that are independent of human land use. Overall, our study has unravelled some systematic structures of soil food-webs, which extends our mechanistic understanding how environmental characteristics of the soil ecosystem determine patterns at the community level.

Recent research suggests that effects of species loss on the structure and functioning of ecosystems willcritically depend on the order with which species go extinct. However, there are few studies of theresponse of natural ecosystems to realistic extinction sequences. Using an extinction scenario basedon the International Union for Conservation of Nature (IUCN) Red List, de Visser et al. sequentiallydeleted species from a topological model of the Serengeti food web. Under this scenario, large-bodiedspecies like top predators and mega-herbivores go extinct first. The resulting changes in the trophicstructure of the food web might affect the robustness of the ecosystem to future disturbances.

Owing to interdependences among species in ecological communities, the loss of one species can trigger a cascade of secondary extinctions with potentially dramatic effects on the functioning and stability of the community. It is, therefore, important to assess the risk and likely extent of secondary extinctions. Community viability analysis is a new technique that can be used to accomplish this goal. The analysis can also be used to identify fragile community structures and keystone species and, hence, to provide guidelines for conservation priorities. Here, we describe the principles underlying community viability analysis and review its contributions to our understanding of the response of ecological communities to species loss.

The loss of a species from an ecological community can set up a cascade of secondary extinctions that in the worst case could lead to the collapse of the community. Both deterministic and stochastic mechanisms may be involved in such secondary extinctions. To investigate the extent of secondary extinctions in ecological communities following the loss of a species, we here develop a community viability analysis. We introduce a measure called the “quasi-collapse risk” that is defined as the probability that the number of species in a community falls below some defined value within a fixed period of time following the loss of a species. We develop deterministic and stochastic methods for finding post-extinction communities. We use these methods to investigate the relationship between diversity (species richness) and quasi-collapse risks in model communities. It is shown that, in a deterministic context, communities with more species within trophic levels have a larger fraction of species remaining in post-extinction communities. This benefit of species richness is to a large extent lost in the presence of demographic stochasticity. The reason for this is a negative relationship between population density and species diversity. We also show that communities become increasingly triangular in shape as secondary extinctions take place, due to greater extinction risk of species at higher trophic levels. We argue that this new approach holds some promise for identifying fragile ecosystems and keystone species.

The non-specific lipid transfer proteins (nsLTP) are unique to land plants. The nsLTPs are characterized by a compact structure with a central hydrophobic cavity and can be classified to different types based on sequence similarity, intron position or spacing between the cysteine residues. The type G nsLTPs (LTPGs) have a GPI-anchor in the C-terminal region which attaches the protein to the exterior side of the plasma membrane. The function of these proteins, which are encoded by large gene families, has not been systematically investigated so far. In this study we have explored microarray data to investigate the expression pattern of the LTPGs in Arabidopsis and rice. We identified that the LTPG genes in each plant can be arranged in three expression modules with significant coexpression within the modules. According to expression patterns and module sizes, the Arabidopsis module AtI is functionally equivalent to the rice module OsI, AtII corresponds to OsII and AtIII is functionally comparable to OsIII. Starting from modules AtI, AtII and AtIII we generated extended networks with Arabidopsis genes coexpressed with the modules. Gene ontology analyses of the obtained networks suggest roles for LTPGs in the synthesis or deposition of cuticular waxes, suberin and sporopollenin. The AtI-module is primarily involved with cuticular wax, the AtII-module with suberin and the AtIII-module with sporopollenin. Further transcript analysis revealed that several transcript forms exist for several of the LTPG genes in both Arabidopsis and rice. The data suggests that the GPI-anchor attachment and localization of LTPGs may be controlled to some extent by alternative splicing.

Loss of biodiversity is one of the most severe threats to the ecosystems of the world. The major causes behind the high population and species extinction rates are anthropogenic activities such as overharvesting of natural populations, pollution, climate change and destruction and fragmentation of natural habitats. There is an urgent need of understanding how these species losses affect the ecological structure and functioning of our ecosystems. Ecological communities exist in a landscape but the spatial aspects of community dynamics have until recently to large extent been ignored. However, the community’s response to species losses is likely to depend on both the structure of the local community as well as its interactions with surrounding communities. Also the characteristics of the species going extinct do affect how the community can cope with species loss. The overall goal of the present work has been to investigate how both local and regional processes affect ecosystem stability, in the context of preserved biodiversity and maintained ecosystem functioning. The focus is particularly on how these processes effects ecosystem’s response to species loss. To accomplish this goal I have formulated and analyzed mathematical models of ecological communities. We start by analyzing the local processes (Paper I and II) and continue by adding the regional processes (Paper III, IV and V).

In Paper I we analyze dynamical models of ecological communities of different complexity (connectance) to investigate how the structure of the communities affects their resistance to species loss. We also investigate how the resistance is affected by the characteristics, like trophic level and connectivity, of the initially lost species. We find that complex communities are more resistant to species loss than simple communities. The loss of species at low trophic levels and/or with high connectivity (many links to other species) triggers, on average, the highest number of secondary extinctions. We also investigate the structure of the post-extinction community. Moreover, we compare our dynamical analysis with results from topological analysis to evaluate the importance of incorporating dynamics when assessing the risk and extent of cascading extinctions.

The characteristics of a species, like its trophic position and connectivity (number of ingoing and outgoing trophic links) will affect the consequences of its loss as well as its own vulnerability to secondary extinction. In Paper II we characterize the species according to their trophic/ecological uniqueness, a new measure of species characteristic we develop in this paper. A species that has no prey or predators in common with any other species in the community will have a high tropic uniqueness. Here we examine the effect of secondary extinctions on an ecological community’s trophic diversity, the range of different trophic roles played by the species in a community. We find that secondary extinctions cause loss of trophic diversity greater than expected from chance. This occurs because more tropically unique species are more vulnerable to secondary extinctions.

In Paper III, IV and V we expand the analysis to also include the spatial dimension. Paper III is a book chapter discussing spatial aspects of food webs. In Paper IV we analyze how metacommunities (a set of local communities in the landscape connected by species dispersal) respond to species loss and how this response is affected by the structure of the local communities and the number of patches in the metacommunity. We find that the inclusion of space reduces the risk of global and local extinctions and that lowly connected communities are more sensitive to species loss.

In Paper V we investigate how the trophic structure of the local communities, the spatial structure of the landscape and the dispersal patterns of species affect the risk of local extinctions in the metacommunity. We find that the pattern of dispersal can have large effects on local diversity. Dispersal rate as well as dispersal distance are important: low dispersal rates and localized dispersal decrease the risk of local and global extinctions while high dispersal rates and global dispersal increase the risk. We also show that the structure of the local communities plays a significant role for the effects of dispersal on the dynamics of the metacommunity. The species that are most affected by the introduction of the spatial dimension are the top predators.

Abstract [en]

The loss of a species from an ecological community can trigger a cascade of secondary extinctions. Here we investigate how the complexity (connectance) of model communities affects their response to species loss. Using dynamic analysis based on a global criterion of persistence (permanence) and topological analysis we investigate the extent of secondary extinctions following the loss of different kinds of species.

We show that complex communities are, on average, more resistant to species loss than simple communities: the number of secondary extinctions decreases with increasing connectance. However, complex communities are more vulnerable to loss of top predators than simple communities.

The loss of highly connected species (species with many links to other species) and species at low trophic levels triggers, on average, the largest number of secondary extinctions. The effect of the connectivity of a species is strongest in webs with low connectance.

Most secondary extinctions are due to direct bottom-up effects: consumers go extinct when their resources are lost. Secondary extinctions due to trophic cascades and disruption of predator-mediated coexistence also occur. Secondary extinctions due to disruption of predator-mediated coexistence are more common in complex communities than in simple communities, while bottom-up and top-down extinction cascades are more common in simple communities.

Topological analysis of the response of communities to species loss always predicts a lower number of secondary extinctions than dynamic analysis, especially in food webs with high connectance.